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SVMtm specifications

Information


Unique identifier OMICS_07264
Name SVMtm
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dr. Zheng Yuan

Publication for SVMtm

SVMtm citations

 (14)
call_split

The Signature Sequence Region of the Human Drug Transporter Organic Anion Transporting Polypeptide 1B1 Is Important for Protein Surface Expression

2014
PMCID: 4209838
PMID: 25371825
DOI: 10.1155/2014/129849
call_split See protocol

[…] The topology of OATP1B1 was predicted using the online prediction programs TOPCONS [], Phobius [], TMpred [], TopPred II [], Membrain [], PHDhtm [], Split 4.0 [], Philius [], HMMTOP [], SVMtm [], ConPred II [], SOSUI [], TMHMM [], TSeg [], PRED-TMR [], and MEMSAT3 []. A homology model was generated using the Protein Homology/analogY Recognition Engine V 2.0 (PHYRE2) [], which modeled […]

library_books

A Pseudomonas aeruginosa EF Hand Protein, EfhP (PA4107), Modulates Stress Responses and Virulence at High Calcium Concentration

2014
PLoS One
PMCID: 4053335
PMID: 24918783
DOI: 10.1371/journal.pone.0098985

[…] fSeq UniProtKB/Swiss-Prot and HHPred . Functional domains were predicted using PFAM , and PROSITE . The putative signal peptide of PA4107 was predicted using TMHMM 1.0 , SignalIP 4.0 , PrediSi and SVMTM .PA4107 (efhP) was deleted from the chromosomes of PAO1 and FRD1 and replaced with the gentamicin omega fragment using the allelic exchange strategy as described previously . The primers used fo […]

library_books

Comparative Analysis of Putative Orthologues of Mitochondrial Import Motor Subunit: Pam18 and Pam16 in Plants

2013
PLoS One
PMCID: 3806816
PMID: 24194927
DOI: 10.1371/journal.pone.0078400

[…] d Pam16s were predicted to have transmembrane region (). Some of them contain two transmembrane regions, such as SlPam16L4, OsPam16L3 and VvPam16L2. To ensure the quality of these prediction results, SVMtm transmembrane domain predictor was adopted to reconfirm the prediction (). However, some orthologues were not predicted to have TM region according to this online predictor (). This difference c […]

library_books

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

2013
BMC Genomics
PMCID: 3610235
PMID: 23497205
DOI: 10.1186/1471-2164-14-175

[…] genome and from the M. hyopneumoniae 7448 and M. hyorhinis HUB-1 genomes (NC_007332 and NC_014448 entries, respectively) were analyzed using the default parameters by the following software programs: SVMtm Transmembrane Domain Predictor [], TMHMM Server v. 2.0 [], SCAMPI [], and PSORTb []. The first three programs predicted the presence of transmembrane (TM) domains, and the fourth was used for to […]

library_books

Subcellular Localization of Extracytoplasmic Proteins in Monoderm Bacteria: Rational Secretomics Based Strategy for Genomic and Proteomic Analyses

2012
PLoS One
PMCID: 3415414
PMID: 22912771
DOI: 10.1371/journal.pone.0042982

[…] Transmembrane hydrophobic α-helice domain (TMD) were predicted combining (i) TMHMM v2.0 , (ii) SVMtm v1.0 (iii) THUMBUP v1.0 , (iv) SOSUI v1.10 , (v) HMMTOP v2.0 , (vi) PHDhtm v8.94_69 , (vii) UMDHMMTMHP v1.0 , (vii) MEMSAT v3.0 , (ix) MemBrain v1.0 , (x) OCTOPUS v1.0 , (xi) MINNOU v1.0 , (xii […]

library_books

GO PROMTO Illuminates Protein Membrane Topologies of Glycan Biosynthetic Enzymes in the Golgi Apparatus of Living Tissues

2012
PLoS One
PMCID: 3283625
PMID: 22363620
DOI: 10.1371/journal.pone.0031324

[…] ver, a closer inspection of topology predictions revealed that the number of transmembrane domains vary considerably from no transmembrane domain (Minnou, PHDhtm, S-Tmhmm_v0.9, TmHMM_v2, SosuiG_v1.1, SVMtm_v3, THUMBUP_v1, TMMOD) to one transmembrane domain (MemSat_v3, Phobius, PredTmr_v1, Scampi, Alom_v2, DAS-TMfilter, Eiconda_v1), two transmembrane domains (TmPred, TopPred_v2), and three transmem […]

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SVMtm institution(s)
ARC Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia

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